After the Sonderbund War of 1847, there were deep social rifts in in the canton of Lucerne between the liberals on the one side and the Catholic-conservatives on the other. This was a conflict between two very different concepts of society: the one liberal, secular and modern; the other Catholic-conservative and traditional. This polarisation directly drew in the Higher Education Institution, no less because the appointment of the Jesuits had actually caused the conflict to escalate externally after 1844. The canton remained under liberal rule until 1871, resulting in several professorial posts being filled by liberal clergymen.

Politically the underdogs, but still strong in the countryside, the conservatives retained their somewhat distrustful oppositional attitude. This stance hindered economic and social development because its proponents sought their identity in the turn towards a traditionally rural life. It also hindered the development of a school system that focussed more on industry and technology and that was geared to the needs of the times. In Lucerne, education was not considered a centrally important resource. While Zurich, Lausanne and Bern had been developing their traditional higher education institutions into universities since the 1830s, Lucerne persisted in maintaining the status quo in education. The elimination of illiteracy was considerably delayed by resistance to the enforcement of compulsory education and by the poor quality of teacher training. A rift soon opened up regarding higher education and science, because up until 1889 all Swiss universities were located in liberal cities that had traditionally been reformed. As in other countries, the differences soon became apparent, so much so, that there was talk of a real 'Catholic inferiority', i.e. an educational deficit.

In the second half of the 19th century, the ideological contrasts prompted numerous conflicts. Whilst the liberals stood up for a secular society, the conservatives saw themselves as the guarantors of a counter-enlightened Catholic order. As had already been the case in the 1830s, church politics thereby again became a battleground. The programmatically anti-liberal stance of the Pope, of large sections of the clergy and of church-goers alike, allowed cultural struggles to erupt. The state limited clerical influence to the best of its ability, and the Catholic conservatives organized themselves as an opposition bloc. The First Vatican Council of 1870, which declared papal infallibility, led to a split. The liberal wing within the Catholic community constituted itself as an independent church. One of its most important proponents, who would later become its first Swiss bishop, was Eduard Herzog. Herzog came from Schongau and worked in Lucerne as a professor for Bible and canon law. Two other professors personally opposed the Council's decisions but subjected their own convictions to these rulings. These events marked the beginning of a new orientation: within a few years, the teaching staff of the Theological Institute were strictly conservative. The bishop made the prospective theologians leave the existing student fraternity 'Semper Fidelis'; they thus had to reorganize themselves and joined together again in the 'Waldstättia'.

Shortly before the open outbreak of the culture war, the government in Solothurn had closed the Seminary there. When the police also deported the bishop, and he sought refuge in the canton of Lucerne, he was able to effectively present himself as a victim of state persecution. This led to a broad show of solidarity, also from outside Switzerland; a large-scale collection of donations became a success. These donations made it possible for the bishop to construct a large building of its own for the Lucerne seminary at 15 Adligenswilerstrasse. In 1971, this old seminary was replaced by a new building designed by the architect Walter Rüssli, and it still stands there today. In 1890, the Lucerne government moved the upper department of the Higher Education Institution to the building in Adligenswilerstrasse. Initially, the upper department retained its connection with the Lucerne Gymnasium – up and until 1910, a single principal was responsible for both parts. The merger on one and the same location with the seminary for priests meant that the study of theology was directed towards practical pastoral care. This was tantamount to renouncing theology as an academic discipline. At the same time, there was another decisive obstacle to the establishment of an academic institution: in 1889, as a result of the culture war, the canton of Fribourg founded its own university in a par force action. This was a clear signal: since then, Fribourg has claimed to be the primary and only place in Switzerland offering a university education in the true Catholic spirit. For the foreseeable future, there was therefore no place for Lucerne, which adhered to the same ideological and political orientation